rs1565488

Positions:

• chr6-68475863-G-A
• chr6-68475863-G-C
• chr6-68475863-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.713 in 151,750 control chromosomes in the GnomAD database, including 39,369 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.71 (39369 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68475863G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288088	ENST00000654495.1	n.235+36926C>T		intron_variant
ENSG00000288088	ENST00000657302.1	n.111+100182C>T		intron_variant
ENSG00000288088	ENST00000669267.1	n.86-8614C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108191 AN: 151632 Hom.: 39352 Cov.: 30

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.745

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.713 AC: 108255 AN: 151750 Hom.: 39369 Cov.: 30 AF XY: 0.715 AC XY: 52999 AN XY: 74162

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.745

Alfa AF: 0.749 Hom.: 15464

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1565488; hg19: chr6-69185755; COSMIC: COSV69403346;